WASHINGTON (CNN) --A top Pentagon intelligence official who has been criticized for remarks he made about Muslims issued a statement Friday to clarify his comments and offer an apology.

Lt. Gen. William Boykin, a former head of U.S. Army Special Forces who is now involved in the search for Osama bin Laden, said in a speech to a Christian prayer group in June that radical Muslims hate the United States "because we're a Christian nation, because our foundation and roots are Judeo-Christian and the enemy is a guy named Satan."

He also said that when dealing with a Somali warlord, "I knew that my God was a real God, and his was an idol."

In his statement, Boykin said for 33 years he has defended every American's right to "worship as he or she chooses" and the "right of free speech and a free press."

"I will continue to do so," he said.

Boykin said his primary message to audiences has been to pray for America's leaders. He went on to defend the above statements.

"My comments to Osman Otto in Mogadishu were not referencing his worship of Allah but his worship of money and power; idolatry. He was a corrupt man, not a follower of Islam. My references to Judeo-Christian roots in America or our nation as a Christian nation are historically undeniable," the statement said.

He concluded with an apology.

"For those who have been offended by my statements, I offer a sincere apology," he said.

But the Council on American-Islamic relations said Boykin's continued involvement in the war on terror sent a negative message to Muslims.

"This apology should be appreciated but the question is, do we want a person with extremist views... in this position in the war on terror," the group's executive director, Nihad Awad, told CNN. "If he continues to be there it sends a very negative message to the Muslim world."

In 1980, Boykin was involved in the failed attempt to rescue U.S. hostages in Iran, and in 1993 he led a deadly raid in Somalia in which U.S. troops were ambushed.